Oblique Line Scanner Systems and Methods for High Throughput Single Molecule Tracking in Living Cells

This application is a continuation of International Application No. PCT/US2023/085592, filed Dec. 21, 2023, which claims priority to U.S. Provisional Application No. 63/476,953, filed Dec. 22, 2022, and U.S. Provisional Application No. 63/476,942, filed Dec. 22, 2022, the contents of each of which are incorporated herein by reference herein in their entirety.

The subject matter described herein relates to a platform to track single molecules within complex systems.

The movement of proteins within the crowded environment of living cells are profoundly influenced by interactions with their surroundings. Single molecule tracking (SMT) is one method for capturing protein movement as a reporter of activity. In SMT, a fluorescent protein of interest is imaged at high spatiotemporal resolution to track its movement in a complex system, e.g., a live cell. The information embedded in these tracks has been used to investigate diverse cellular phenomena including protein-protein interactions, e.g., interactions mediating signal transduction, inter-organelle communication, nuclear organization, and transcription regulation. The application of SMT techniques has been limited in scale, however, and therefore mainly used to address specific mechanistic hypotheses. For example, SMT has not been adapted to a throughput setting that would enable systems-level screening or drug discovery.

In a first aspect, the present disclosure is directed to a method of determining whether a compound that induces a change in binding of a target fluorescent protein in a live cell reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in a detected field of view of the sample plane via a detector device, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, and wherein the method is adapted to selectively detect localized fluorescence; and (c) determining a change in the movement of the target fluorescent protein in the presence of the compound; wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a method of determining whether a compound that induces a change in binding of a target fluorescent protein in a live cell reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells, wherein the subset of the of the target fluorescent proteins produces up to about 1,000,000 molecular trajectories in a single detected field of view; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in the detected field of view of the sample plane via a detector device, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, and wherein the method is adapted to selectively detect localized fluorescence; and (c) determining a change in the movement of the target fluorescent protein in the presence of the compound; wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a method of determining whether a compound that induces a change in binding of a target fluorescent protein in a live cell reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in a detected field of view of the sample plane via a detector device, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, and wherein the method is adapted to selectively detect localized fluorescence relative; and (c) determining a change in the movement of the target fluorescent protein in the presence of the compound; wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a method of determining whether a compound that induces a change in binding of a target fluorescent protein in a live cell reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in a detected field of view of the sample plane via a detector device, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, wherein equal to or greater than 95% of the detected field of view achieves sufficient laser illumination for tracking protein movement, and wherein the method is adapted to selectively detect localized fluorescence; and (c) determining a change in the movement of the target fluorescent protein in the presence of the compound; wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In certain instances of the above aspects, the change in movement detected is an increase in immobile trajectories indicating an increase in the occupation or duration of the bound state (f) of the target fluorescent protein. In certain instances of the above aspects, the change in movement detected is a change in: (a) the median of the jump length distribution; (b) 3quartile of the jump length distribution; (c) median radius of gyration; (d) mean posterior diffusion coefficient; (e) geometric mean posterior diffusion coefficient; (f) mean squared displacement; (g) median bond angle; (h) diffusion coefficient maximum likelihood estimator; and/or (i) state occupation via inference. In certain instances of the above aspects, the target fluorescent protein interacts in a larger molecular assembly. In certain instances of the above aspects, the target fluorescent protein is a ligand. In certain instances of the above aspects, the target fluorescent protein is a receptor. In certain instances of the above aspects, the biological interaction is a direct interaction. In certain instances of the above aspects, the direct interaction comprises binding of the compound to the target fluorescent protein. In certain instances of the above aspects, the biological interaction is an indirect interaction. In certain instances of the above aspects, the indirect interaction comprises the compound agonizing or antagonizing a larger molecular assembly comprising the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a method of determining a dose of a compound that induces a change in binding of a target fluorescent protein in a live cell by determining that the compound reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in a detected field of view of the sample plane via a detector device wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, and wherein the method is adapted to selectively detect localized fluorescence; and (c) determining a dose by determining a change in the movement of the target fluorescent protein in the presence of the compound; and wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a method of determining a dose of a compound that induces a change in binding of a target fluorescent protein in a live cell by determining whether the compound reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells, wherein the subset of the of the target fluorescent proteins produces up to about 1,000,000 molecular trajectories in a single detected field of view; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in the detected field of view of the sample plane via a detector device, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, and wherein the method is adapted to selectively detect localized fluorescence; and (c) determining a dose by determining a change in the movement of the target fluorescent protein in the presence of the compound; and wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a method of determining a dose of a compound that induces a change in binding of a target fluorescent protein in a live cell by determining that the compound reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in a detected field of view of the sample plane via a detector device, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, and wherein the method is adapted to selectively detect localized fluorescence; and (c) determining a dose by determining a change in the movement of the target fluorescent protein in the presence of the compound; and wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a method of determining a dose of a compound that induces a change in binding of a target fluorescent protein in a live cell by determining that the compound reduces the Kof the target fluorescent protein comprising: (a) contacting a sample comprising a population of live cells with the compound, where the live cells comprise the target fluorescent protein; (b) tracking the movement of individual target fluorescent proteins in a plurality of the cells in the sample, wherein said tracking comprises: (i) illuminating a field of view in a sample plane disposed within the sample with a light beam to cause fluorescence by at least a subset of the target fluorescent proteins in the live cells; (ii) detecting the fluorescence from one or more of the target fluorescent proteins in a detected field of view of the sample plane via a detector device wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, wherein equal to or greater than 95% of the detected field of view achieves sufficient laser illumination for tracking protein movement, and wherein the method is adapted to selectively detect localized fluorescence; and (c) determining a dose by determining a change in the movement of the target fluorescent protein in the presence of the compound; and wherein an increase in the signal detected from the target fluorescent protein in the presence of the compound relative to the signal of the target fluorescent protein in the absence of the compound indicates that the compound induces a reduction in the Kof the target fluorescent protein.

In certain instances of the above aspects, the change in movement detected is an increase in immobile trajectories indicating an increase in bound (f) target fluorescent protein. In certain instances of the above aspects, the change in movement detected is a change in: (a) the median of the jump length distribution; (b) 3quartile of the jump length distribution; (c) median radius of gyration; (d) mean posterior diffusion coefficient; (e) geometric mean posterior diffusion coefficient; (f) mean squared displacement; (g) median bond angle; (h) diffusion coefficient maximum likelihood estimator; and/or (i) state occupation via inference. In certain instances of the above aspects, the target fluorescent protein interacts in a larger molecular assembly. In certain instances of the above aspects, the target fluorescent protein is a ligand. In certain instances of the above aspects, the target fluorescent protein is a receptor. In certain instances of the above aspects, the biological interaction is a direct interaction. In certain instances of the above aspects, the direct interaction comprises binding of the compound to the target fluorescent protein In certain instances of the above aspects, the biological interaction is an indirect interaction. In certain instances of the above aspects, the indirect interaction comprises the compound agonizing or antagonizing a larger molecular assembly comprising the target fluorescent protein.

In an interrelated aspect, the present disclosure is directed to a microscopy system configured to determine whether a compound that induces a change in binding of a target fluorescent protein in a cell reduces the Kof the target fluorescent protein comprising: (a) a stage for supporting a sample, wherein the sample comprises a population of cells, and where the cells comprise the target fluorescent protein; (b) a light source for emitting a light beam capable of inducing a light-based response from a plurality of the target fluorescent proteins in the sample; (c) an objective for focusing the light beam on the sample in the sample plane, wherein a subset of the target fluorescent proteins in the sample are disposed in a detected field of view in the sample plane, and wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension; (d) a detector device for monitoring the light-based response from the target fluorescent proteins in the presence of the compound; (e) a memory; and (f) a processor in communication with the memory and the detector device, where the processor is capable of determining the change in the movement of the target fluorescent protein in the presence of the compound.

In an interrelated aspect, the present disclosure is directed to a microscopy system configured to determine whether a compound that induces a change in binding of a target fluorescent protein in a cell reduces the Kof the target fluorescent protein comprising: (a) a stage for supporting a sample, wherein the sample comprises a population of cells, and where the cells comprise the target fluorescent protein; (b) a light source for emitting a light beam capable of inducing a light-based response from a plurality of the target fluorescent proteins in the sample; (c) an objective for focusing the light beam on the sample in the sample plane, wherein a subset of the target fluorescent proteins in the sample are disposed in a detected field of view in the sample plane, and wherein the subset of the of the target fluorescent proteins produces up to about 1,000,000 molecular trajectories in a single detected field of view and wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension; (d) a detector device for monitoring the light-based response from the target fluorescent proteins in the presence of the compound; (e) a memory; and (f) a processor in communication with the memory and the detector device, where the processor is capable of determining the change in the movement of the target fluorescent protein in the presence of the compound.

In an interrelated aspect, the present disclosure is directed to a microscopy system configured to determine whether a compound that induces a change in binding of a target fluorescent protein in a cell reduces the Kof the target fluorescent protein comprising: (a) a stage for supporting a sample, wherein the sample comprises a population of cells, and where the cells comprise the target fluorescent protein; (b) a light source for emitting a light beam capable of inducing a light-based response from a plurality of the target fluorescent proteins in the sample; (c) an objective for focusing the light beam on the sample in the sample plane, wherein a subset of the target fluorescent proteins in the sample are disposed in a detected field of view in the sample plane, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension; (d) a detector device for monitoring the light-based response from the target fluorescent proteins in the presence of the compound; (e) a memory; and (f) a processor in communication with the memory and the detector device, where the processor is capable of determining the change in the movement of the target fluorescent protein in the presence of the compound relative to the absence of the compound.

In an interrelated aspect, the present disclosure is directed to a microscopy system configured to determine whether a compound that induces a change in binding of a target fluorescent protein in a cell reduces the Kof the target fluorescent protein comprising: (a) a stage for supporting a sample, wherein the sample comprises a population of cells, and where the cells comprise the target fluorescent protein; (b) a light source for emitting a light beam capable of inducing a light-based response from a plurality of the target fluorescent proteins in the sample; (c) an objective for focusing the light beam on the sample in the sample plane, wherein a subset of the target fluorescent proteins in the sample are disposed in a detected field of view in the sample plane, wherein the detected field of view has a size of about 150 μm to about 250 μm in a first dimension by about 100 μm to about 210 μm in a second dimension, and wherein equal to or greater than 95% of the detected field of view achieves sufficient laser illumination for tracking protein movement; (d) a detector device for monitoring the light-based response from the target fluorescent proteins in the presence of the compound; (e) a memory; and (f) a processor in communication with the memory and the detector device, where the processor is capable of determining the change in the movement of the target fluorescent protein in the presence of the compound

In certain instances of the above aspects, the change in movement detected is an increase in immobile trajectories indicating an increase in bound (f) target fluorescent protein. In certain instances of the above aspects, the change in movement detected is a change in: (a) the median of the jump length distribution; (b) 3quartile of the jump length distribution; (c) median radius of gyration; (d) mean posterior diffusion coefficient; (e) geometric mean posterior diffusion coefficient; (f) mean squared displacement; (g) median bond angle; (h) diffusion coefficient maximum likelihood estimator; and/or (i) state occupation via inference. In certain instances of the above aspects, the target fluorescent protein interacts in a larger molecular assembly. In certain instances of the above aspects, the target fluorescent protein is a ligand. In certain instances of the above aspects, the target fluorescent protein is a receptor. In certain instances of the above aspects, the biological interaction is a direct interaction. In certain instances of the above aspects, the direct interaction comprises binding of the compound to the target fluorescent protein. In certain instances of the above aspects, the biological interaction is an indirect interaction. In certain instances of the above aspects, the indirect interaction comprises the compound agonizing or antagonizing a larger molecular assembly comprising the target fluorescent protein.

The presently disclosed subject matter relates to the development of industrial-scale, high-throughput SMT (htSMT) techniques employing oblique line scanning (OLS) illumination, systems incorporating such OLS htSMT techniques, hardware and software related to such OLS htSMT techniques, as well as methods of using such OLS htSMT techniques. For example, the OLS htSMT techniques described herein are capable of measuring protein movement in millions of cells per day. In addition to the ability to capture a large number of cells per field of view, OLS benefits from an improved spatial homogeneity in signal to noise ratio (SNR) across the camera chip, better confocality (less out of focus signal and reduced motion blurring) and higher temporal resolution, e.g., as outlined in Table 1 (where each “+” represents a 2-fold improvement).

The OLS htSMT techniques described herein can be used for a variety of applications including, but not limited to, drug discovery activities, such as compound library screening and the elucidation of structure-activity relationships (SAR). Importantly, the OLS htSMT techniques described herein can be used to characterize both known and novel pathway contributions to larger molecular assemblies comprising the target, such as protein signaling interaction networks.

With reference to, aspects of the current subject matter can be implemented using an OLS htSMT workflow. This workflow can include various phases, as will be described in further detail below, such as (i) sample preparation including reagent handling, (ii) image acquisition using imaging of the samples to generate a series of images and/or videos, (iii) image analysis through processing of these images and video using, for example, various analytics, single-emitter detection and sub-pixel localization (i.e., “super resolution imaging”), tracking, computer vision, and machine learning algorithms, (iv) storage of information (i.e., features, raw images, modified images, etc.) extracted from or otherwise characterizing or comprising the images and video, and (v) provision of insights using the stored information including biological interpretation (which can additionally or alternatively be provided using various analytics, tracking, computer vision, and machine learning algorithms).

The subject matter of the present disclosure is described with reference to the figures, where reference numbers are used to designate similar or equivalent elements throughout. The figures are not drawn to scale and they are provided merely to illustrate aspects disclosed herein. Several disclosed aspects are described below with reference to exemplary hardware, software, and applications for illustration. It should be understood that numerous specific details, relationships and methods are set forth to provide a more complete understanding of the subject matter disclosed herein. For purposes of clarity of disclosure and not by way of limitation, the detailed description is divided into the following subsections:

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the presently disclosed subject matter. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.

The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. The singular forms “a,” “an” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other instances “comprising,” “consisting of”, and “consisting essentially of,” the instances or elements presented herein, whether explicitly set forth or not.

For the recitation of numeric ranges herein, each intervening number within the range is explicitly contemplated with the same degree of precision. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the number 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitly contemplated.

As used herein, the term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within 3 or more than 3 standard deviations, per the practice in the art. Alternatively, “about” can mean a range of up to 20%, preferably up to 10%, more preferably up to 5%, and more preferably still up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value.

As used herein the term “trajectory” refers to the set of spatial coordinates corresponding to the position of an observation of fluorescent protein, linked in time. In certain instances, a plurality of trajectories may be constructed algorithmically by linking a plurality of fluorescent proteins whose positions have been determined in successive time points. In certain instances, a plurality of trajectories may be constructed conservatively by linking only spots within a fixed search radius when no other links are plausible. In certain instances, a plurality of trajectories may be constructed probabilistically.

As defined herein, protein movement refers to the change in position of a plurality of fluorescent proteins. In certain instances, protein movement may be quantified by analysis of changes in spatial coordinates in sequential timepoints. Movement characterized in this way may include, but not be limited to, measurements of the jump length distribution: Given a set of protein displacements between one timepoint and a subsequent timepoint, a histogram can be constructed of the probability of each of the displacement lengths (“jump lengths”). Quantiles of this distribution can be used to describe the motion of the protein. In certain instances the quantile used is the median of the jump length distribution. In certain instances, the quantile used is the 3quartile of the jump length distribution. In certain instances, protein movement may be quantified by analysis of trajectories. Movement characterized in this way may include, but not be limited to, measurements of the mean squared displacement as defined by the average of the square of all displacements in a trajectory, averaged over the plurality of trajectories. Movement characterized in this way may also include, but not be limited to, measurements of the trajectory length or distribution of trajectory lengths. Movement characterized in this way may also include, but not be limited to, measurements of the mean radius of gyration, as defined by the root mean square distance of all coordinates in a trajectory from the center of mass of the set of points contained in the trajectory, averaged over the plurality of trajectories. Movement characterized in this way may also include, but not be limited to, measurements of the mean bond angle, defined by the angle formed from three sequential spatial coordinates averaged over the plurality of trajectories. Movement characterized in this way may also include, but not be limited to, measurements of the diffusion coefficient maximum likelihood estimator, defined as an estimate of the maximum likelihood diffusion coefficient for the plurality of trajectories under a single-state diffusion model with constant localization error. In certain instances, protein movement may be measured by measured through analysis of the product of the link-generating algorithm. Movement characterized in this way may include, but not be limited to, the mean posterior diffusion coefficient, the mean of the posterior probability distribution of coefficients from a probabilistic linking algorithm. Movement characterized in this way may include, but not be limited to, the geometric mean posterior diffusion coefficient, the mean of the log-scaled posterior probability distribution of coefficients from a probabilistic linking algorithm. In certain instances, protein movement may be measured by measured through model-dependent analysis of the plurality of trajectories. Movement characterized in this way may include, but not be limited to, the fraction of immobile molecules (“f”) as defined by two-state model fitting.

As used herein, the term “movement” encompasses changes in the direction as well as changes, both increases and decreases, in the speed at which a target is traveling. Accordingly, tracking movement can, in certain instances, include determining that the target is not moving, e.g., when the target either is or is essentially in a static bound state. Movement can be characterized in a variety of ways, including, but not limited to, quantifying: (a) the median of the jump length distribution (where the jump length corresponds to the observed distance the target fluorescent protein travels in consecutive frames); (b) 3rd quartile of the jump length distribution; (c) median radius of gyration; (d) mean posterior diffusion coefficient; (e) geometric mean posterior diffusion coefficient; (f) mean squared displacement; (g) median bond angle; (h) diffusion coefficient maximum likelihood estimator; (i) trajectory length; and/or (j) state occupation via inference.

As used herein, the movement being detected, including, but not limited to, any change in movement, can occur in response to any environmental or other factor. For example, but not by way of limitation, the movement, or lack thereof, can be elicited by: (A) compound addition; (B) a change in temperature; (C) a change in oxygen concentration, e.g., introduction of a hypoxic condition; (D) mechanical stress; (E) a change in pH; and/or (F) a change in light exposure (e.g., increasing or decreasing intensity).

As used herein, the term “fluorescent protein” refers to any protein that emits a fluorescent signal. In certain instances, the fluorescent emission occurs in response to exposure to light of a particular wavelength. An example of a naturally occurring fluorescent protein is Green fluorescent protein (GFP). In certain instances, however, a protein of interest can be adapted to emit a fluorescent signal via the introduction of an encoded fluorescent tag, i.e., a protein sequence is fused to a protein of interest to render it fluorescent. In certain instances, a protein of interest can be adapted to emit a fluorescent signal through binding of a fluorescent ligand. Nonlimiting examples of such encoded fluorescent tags include: Halo tags, SNAP tags, CLIP tags, TMP tags, and SunTags. Additionally, or alternatively, a protein of interest can be adapted to emit a fluorescent signal via coupling the protein to a fluorescent dye molecule, e.g., amine- or sulfhydryl-reactive dyes.

As used herein, the term “compound” refers to any chemically-defined entity. In certain instances, the compound can be a molecule less than 1000 Da, i.e., a “small molecule”. In certain instances, the compound can be a macromolecule such as a nucleic acid. In certain instances, the nucleic acid can have a defined sequence. In certain instances, the nucleic acid comprises; (A) ribonucleic acid (RNA), including, for example, modified RNA; (B) deoxyribonucleic acid (DNA), including, for example, modified DNA; as well as (C) combinations of (A) and (B). In certain instances, the nucleic acid will be a single-stranded or double-stranded small interfering nucleic acid (e.g., a double-stranded siRNA), an antisense oligonucleotide, a ribozyme, a microRNA, or an aptamer. In certain instances, the compound can be a protein. For example, but not by way of limitation, the protein compounds of the present disclosure encompass signaling proteins, e.g., protein hormones, cytokines, kinases, phosphatases, and other enzymes and transcription factors, as well as antibodies, contractile proteins, structural proteins, storage proteins, and transport proteins. In certain instances, a compound can refer to a mixture of molecules, e.g., a mixture of defined composition.

As used herein, the term “uniform intensity” refers, in connection with the intensity of light, e.g., light directed to a sample plane, to light that differs in intensity no more than 5%, in certain instances, 10%, in certain instances, or 15%, in certain instances.

As used herein, the term “uniform intensity” refers, in connection with signal to noise (SNR), to a pixel-wise SNR within a field of view (FOV) where the range of possible values are comprised between 0.5 to 1 standard deviations from the mean SNR.

With reference to, aspects of the current subject matter can be implemented using an htSMT workflow where such workflow incorporates systems for image acquisition. For example, such image acquisition can incorporate the imaging of samples to generate a series of images and/or videos.depicts a schematic of an exemplary image acquisition system of the present disclosure with the X-Z sample plane visible.depicts the same exemplary image acquisition system, but with the Y-Z sample plane visible. The exemplary image acquisition system (-) comprises: a light source (-) configured to emit light relayed by one or more optical elements in an optical relay (-), the optical relay being configured to shape the light emitted from the light source to form a shaped beam (-) such that the shaped beam has a uniform intensity across a longer dimension of the linear shape; an optical element, e.g., a galvo mirror (-), configured to translate the shaped beam; and one or more optical elements, e.g., a dichroic mirror (-), configured to direct the shaped beam to an objective (-), whereby a portion of the sample plane (-) is illuminated by an inclined beam (-), resulting in the emission of light from the sample, e.g., fluorescence emission, which is focused by the objective (-), through a series of optical elements, e.g., a lens (-) and an emission filter (-), to an image collection system (-).

With reference to the exemplary image acquisition system of, the system comprises a light source (-) configured to emit light. The light source (-), in certain implementations of the image acquisition systems disclosed herein, can be configured to emit light of a single wavelength. In certain implementations of the image acquisition systems disclosed herein, the light source (-) can be configured to emit light of two, three, four, five, or more individual wavelengths. In certain implementations, the wavelength(s) of light emitted by the light source are predetermined. For example, but not by way of limitation, the wavelength(s) can be predetermined such that the emitted light elicits fluorescence emission when illuminating a sample, e.g., a sample comprising a fluorescent protein. In certain instances, the wavelength(s) employed in connection with the methods described herein will fall within a range of 400 nm to 650 nm. In certain instances, the light source (-) will emit light having a wavelength between 400 nm to, between 550 nm to 565 nm, or between 638 nm to 650 nm. In certain non-limiting implementations, the light source (-) is configured to comprise three lasers with nominal central wavelengths 405 nm, 560 nm, 640 nm that could vary within absorption band of the fluorophores used. In certain instances the 405 nm wavelength is used to excite Hoechst dye. In certain instances, a 560 nm wavelength is used to excite dyes (e.g., JF) attached to HaloTag. In certain instances, a 642 or a 646 nm wavelength is used to excite dyes (e.g., JF) attached to HaloTag.

In certain non-limiting implementations, the light source (-) is used to catalyze photochemical reactions. For example, but not by way of limitation, the wavelength(s) and illumination intensities can be such that cleavage of a chemical bond occurs. As an additional example, but not by way of limitation, the wavelength(s) and illumination intensities may induce the adoption of a non-radiative dark state (i.e., “photobleached molecule”). As an additional example, but not by way of limitation, the wavelength(s) and illumination intensities may induce radiative or non-radiative energy transfer between fluorophores within the sample.

In certain implementations of the image acquisition systems described herein, the light source (-) can be configured to deliver a predetermined amount of power to the back focal plane of the objective (-). For example, but not by way of limitation, the light source (-) delivers greater than 10 mW with respect to certain wavelengths, e.g., 405 nm, and/or greater than 150 mW with respect to other wavelengths, e.g., 640 nm. Additionally, or alternatively, in instances where the light source (-) comprises three lasers emitting at 405 nm, 560 nm, and 640 nm wavelengths, respectively the light source (-) can be configured to deliver predetermined amounts of power, to the back focal plane of the objective (-). For example, but not by way of limitation the 405 nm can be configured to deliver >10 mW; the 560 nm can be configured to deliver >150 mW; and the 640 nm can be configured to deliver >50 mW).

In certain implementations of the image acquisition systems described herein, the light source (-) is configured to emit pulsed light. For example, but not by way of limitation, the light source (-) can be configured to emit stroboscopic pulsed light. In certain implementations of the image acquisition systems described herein, the light source (-) is configured to emit pulsed light in synchrony with the start of image acquisition. In certain, non-limiting implementations, the light source (-) will pulse at specific time intervals depending on the number of frames per second being captured. For example, but not by way of limitation, if 100 Frames Per Second (FPS) are being captured by the detector (-), the laser is ON for 9 ms and OFF for 1 ms. In contrast, in 200 FPS mode, the laser is ON for 4 ms OFF for 1 ms. In certain implementations of the OLS htSMT workflow, the light source is configured to go from 90% to 10% power in less than about 0.4 ms. In certain implementations of the OLS htSMT workflow, the light source is configured to go from 90% to 10% power in less than about 0.2 ms.

The emission of light by the light source (-) and the direction of that light to the optical relay (-), can, in certain implementations of the image acquisition systems disclosed herein, be facilitated using a single mode fiber. Alternatively, a multimode fiber can be employed in certain implementations of the image acquisition systems disclosed herein. For example, but not by way of limitation, the multimode fiber can be configured with a predetermined shape for sample illumination.

In certain implementations of the image acquisition systems described herein, for example with respect to systems configured for high throughput sample analysis, the light source (-) can be configured to exhibit low drift in power output. In certain implementations, such low drift configurations increase sample processing consistency to facilitate high throughout analyses. For example, but not by way of limitation, such low drift power output configurations maintain power output within about 0% to about 15% variation, about 0% to about 10% variation, about 10% variation, about 9% variation, about 8% variation, about 7% variation, about 6% variation, about 5% variation, about 4% variation, about 3% variation, about 2% variation or about 1% variation.

In certain instances, such low drift power output configurations maintain power output within about 0% to about 15% variation, about 0% to about 10% variation, about 10% variation, about 9% variation, about 8% variation, about 7% variation, about 6% variation, about 5% variation, about 4% variation, about 3% variation, about 2% variation or about 1% variation in the context of changing ambient (room) temperature, e.g., 17° C.+/−5° C. In certain instances, this is achieved using temperature sensors and/or close-loop heaters to maintain internal light source (e.g., laser engine) temperatures stable, thereby reducing output power drift. For example, but not by way of limitation, the light source can be thermally insulated from the fluctuations of the ambient temperature using an insulated enclosure design. Additionally, or alternatively, closed-loop heaters can be strategically placed at specific locations in the system, e.g., the fiber coupler to reduce output drift. Additionally, or alternatively, water jackets and/or chillers can be used to reduce heat build-up from the laser heads. Moreover, these thermal controls, used individually or in combination, result in shorter warm up times to reach operating steady state and maintained more stable internal operating temperatures when lasers would be powered off and on.

With reference to the exemplary image acquisition system of, the system comprises a light source (-) configured to emit light, which is relayed by one or more optical elements in an optical relay (-), the optical relay being configured to shape the light emitted from the light source to form a shaped beam (-). The particular optical elements of any particular optical relay (-) implementation can be selected and configured to produce the appropriately shaped beam (-) as well as provide for the appropriate translation of that beam.

In certain, non-limiting, implementations of the optical relay (-) of the presently disclosed image acquisition systems, the optical relay (-) will comprise one or more lenses and/or other optical elements. For example, but not by way of limitation, the selection and orientation of lenses and other optical elements in the optical relay (-) will be configured to appropriately shape the light beam being directed to the sample. In certain non-limiting implementations, the optical relay (-) will comprise optical elements to collimate the emitted light, e.g., a collimator (-), from the light source (-). Additionally, or alternatively, the optical relay (-) will comprise additional optical elements, e.g., a Powell lens (-) or other elements adapted to produce a beam fan, one or more cylinder lenses ((-) and (-)), one or more slits to adjust light sheet extent ((-) and (-)), one or more achromatic lenses ((-) and (-)) and/or one or more mirrors ((-), (-) and (-)), one or more of which can be a galvo mirror (-) capable of translating the light. The particular attributes of the optical element will be predetermined to produce an appropriately shaped light beam. For example, but not by way of limitation, the OLS htSMT systems of the present disclosure can achieve uniform horizontal FOV as well as uniform vertical FOV. Such uniformity in horizontal and vertical FOVs contrasts with other strategies that provide non-uniform horizontal FOV and/or non-uniform vertical FOV (See Table 2.)

To achieve uniform horizontal FOV as well as uniform vertical FOV, the optical relay (-) of the OLS htSMT systems described herein comprise an optical element or assembly capable of producing a beam that is elongated along the X plane, and narrow along Y plane and wherein the light beam has a uniform intensity across a longer dimension of the linear shape. In certain non-limiting implementations, the optical relay (-) of the OLS htSMT systems described herein will comprise a Powell lens (-) to shape the light beam such that it has a uniform intensity across a longer dimension of the linear shape (-). The optical relay (-) of the OLS htSMT systems described herein can comprise additional or alternative optical elements or assemblies to shape the light beam such that it has a uniform intensity across a longer dimension of the linear shape (-). For example, but not by way of limitation, the optical relay (-) of the OLS htSMT systems described herein can comprise a diffraction element or assembly configured to shape the light beam such that it has a uniform intensity across a longer dimension of the linear shape.

In certain, non-limiting implementations of the optical relays (-) of the presently disclosed image acquisition systems, the optical relay (-) will comprise one or more optical elements or assemblies configured to translate the light beam relative to the sample plane of the sample to be analyzed, e.g., in a direction orthogonal to the longer dimension of the light beam. For example, but not by way of limitation, such optical elements or assemblies configured to translate the light beam relative to the sample plane of the sample to be analyzed can comprise a galvo mirror (-) or a piezo element configured to translate the light beam. Additionally, or alternatively, such optical elements or assemblies configured to translate the light beam relative to the sample plane of the sample to be analyzed can comprise a computer-controlled motor.

With reference to the exemplary image acquisition system of, the system comprises an optical relay (-) configured to shape the light emitted from the light source to form a shaped beam (-), which is then directed by an optical element (-), e.g., a dichroic mirror, configured to direct the shaped beam to an objective (-), whereby the sample plane (-) is illuminated by an inclined beam (-).

In certain, non-limiting implementations of the image acquisition systems of the present disclosure, an objective (-) directs the inclined beam (-) on the sample plane (-) to be analyzed. In certain, non-limiting implementations of the image acquisition systems of the present disclosure the objective (-) is a water immersion objective. The use of a water immersion objective facilitates high throughput sample analysis by eliminating the oil present in connection with the use of oil immersion objectives, thereby allowing for higher image quality and less distortion. Not only does the presence of oil present issues in the context of automated systems, where the oil can spread to components, including optical elements that can be fouled by exposure to oil, water-immersion objectives are better index-matched for imaging cells, resulting in less distortion and thus higher image quality than with oil objectives. In certain, non-limiting implementations, the objective 60×1.27 NA water immersion objective (Nikon). In certain implementations of the workflows described herein, the water immersion objective (-) will be heated by a heating element. For example, such heating element will maintain the water immersion objective (-) at a temperature sufficient to avoid inducing a change in temperature of the sample contained in the sample plate (-).